Major challenges faced by the human population in recent times include population increase, resource depletion and deterioration of environmental quality. The scarcity of food for the rising population is a critical issue faced by the world in wake of the unpredicted change in climatic conditions. The aquaculture industry plays an important role in solving global food scarcity. It is projected that the share of fish for human consumption originating from aquaculture is projected to increase from 52% (average for the period 2016–2018) to 58% in 2028. The major adverse impact of the traditional aquaculture systems includes the effect on water quality and secondary pollution causing serious damage to the aquatic resources. Improving water recycling efficiency and reducing the discharge of wastewater are the major factors contributing to sustainable aquaculture system. The present study compares the various aquaculture wastewater treatment technologies and their role in achieving sustainability. Recirculation systems in aquaculture units are found to be more effective in managing the volume of wastewater since only 10% of the total volume of water is replaced per day and hence more sustainable. Constructed wetland systems have reported high efficiency in the treatment of wastewater containing nitrogen compounds with NH4-N removal of 86—98% and NO2-N removal efficiency exceeds 99%. The cumulative energy demand of RAFT (Rafter System) and MFBS (Media-Filled Beds System) in Coupled Aquaponics Systems (CAPS) has been reduced to 46.8% and 53.2% which is very less than conventional units. The study of the use of local and low trophic level biomass like microalgae as feedstock was found to reduce the environmental impacts of fish farming with added benefit of biomass production and lipid production. The algae harvesting efficiency of above 90% has been achieved by using proper coagulants in various units. The study of integrated multi-trophic aquaculture operation, combining fed aquaculture with organic extractive aquaculture was found to improve the shellfish output by 20%, and profit was over 230% and 68% greater than that in finfish and shellfish isolated monocultures. The development of more efficient reactor systems and a holistic, integrated approach to wastewater treatment can ensure sustainable aquaculture systems which helps to maintain sustainability in the water -food -energy system.